public int setup(String arg, ImagePlus imp) {
this.arg = arg;
this.imp = imp;
IJ.register(ParticleAnalyzer.class);
if (imp == null) {
IJ.noImage();
return DONE;
}
if (imp.getBitDepth() == 24 && !isThresholdedRGB(imp)) {
IJ.error(
"Particle Analyzer",
"RGB images must be thresholded using\n" + "Image>Adjust>Color Threshold.");
return DONE;
}
if (!showDialog()) return DONE;
int baseFlags = DOES_ALL + NO_CHANGES + NO_UNDO;
int flags = IJ.setupDialog(imp, baseFlags);
processStack = (flags & DOES_STACKS) != 0;
slice = 0;
saveRoi = imp.getRoi();
if (saveRoi != null && saveRoi.getType() != Roi.RECTANGLE && saveRoi.isArea())
polygon = saveRoi.getPolygon();
imp.startTiming();
nextFontSize = defaultFontSize;
nextLineWidth = 1;
return flags;
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
Calibration cal = imp.getCalibration();
GenericDialog gd = new GenericDialog("Options");
int subsize = 32;
gd.addNumericField("Subregion Size (pixels)?", subsize, 0);
int stepsize = 16;
gd.addNumericField("Step Size?", stepsize, 0);
int shift = 3;
gd.addNumericField("STICS temporal Shift?", shift, 0);
float xoffset = 0.0f;
gd.addNumericField("X_Offset", xoffset, 5, 15, null);
float yoffset = 0.0f;
gd.addNumericField("Y_Offset", yoffset, 5, 15, null);
float multiplier = 8.0f;
gd.addNumericField("Velocity Multiplier", multiplier, 5, 15, null);
float ftime = 1.0f;
gd.addNumericField("Frame_Time(min)", ftime, 5, 15, null);
float scaling = (float) cal.pixelWidth;
gd.addNumericField("Pixel_Size(um)", scaling, 5, 15, null);
boolean norm = true;
gd.addCheckbox("Normalize_Vector_lengths?", norm);
boolean centered = true;
gd.addCheckbox("Center_Vectors?", centered);
float magthresh = 0.0f;
gd.addNumericField("Magnitude_Threshhold?", magthresh, 5, 15, null);
int rlength = 10;
gd.addNumericField("Running_avg_length", rlength, 0);
int inc = 5;
gd.addNumericField("Start_frame_increment", inc, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
subsize = (int) gd.getNextNumber();
stepsize = (int) gd.getNextNumber();
shift = (int) gd.getNextNumber();
xoffset = (float) gd.getNextNumber();
yoffset = (float) gd.getNextNumber();
multiplier = (float) gd.getNextNumber();
ftime = (float) gd.getNextNumber();
scaling = (float) gd.getNextNumber();
norm = gd.getNextBoolean();
centered = gd.getNextBoolean();
magthresh = (float) gd.getNextNumber();
rlength = (int) gd.getNextNumber();
inc = (int) gd.getNextNumber();
int width = imp.getWidth();
int xregions = 1 + (int) (((float) width - (float) subsize) / (float) stepsize);
int newwidth = xregions * subsize;
int height = imp.getHeight();
int yregions = 1 + (int) (((float) height - (float) subsize) / (float) stepsize);
int newheight = yregions * subsize;
ImageStack stack = imp.getStack();
int slices = imp.getNSlices();
int channels = imp.getNChannels();
int frames = imp.getNFrames();
if (frames == 1) {
frames = slices;
slices = 1;
}
Roi roi = imp.getRoi();
if (roi == null) {
roi = new Roi(0, 0, width, height);
}
STICS_map map = new STICS_map(subsize, stepsize);
Object[] tseries = jutils.get3DTSeries(stack, 0, 0, frames, slices, channels);
map.update_STICS_map(tseries, width, height, 0, rlength, roi.getPolygon(), shift);
FloatProcessor fp =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
ImageStack vector_stack = new ImageStack(fp.getWidth(), fp.getHeight());
vector_stack.addSlice("", fp);
float[][] vel = map.get_scaled_velocities(scaling, ftime, stepsize);
ImageStack velstack = new ImageStack(map.xregions, map.yregions);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
int velframes = 2;
IJ.showStatus("frame " + 0 + " calculated");
for (int i = inc; i < (frames - rlength); i += inc) {
map.update_STICS_map(tseries, width, height, i, rlength, roi.getPolygon(), shift);
FloatProcessor fp2 =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
vector_stack.addSlice("", fp2);
vel = map.get_scaled_velocities(scaling, ftime, stepsize);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
velframes += 2;
IJ.showStatus("frame " + i + " calculated");
}
(new ImagePlus("STICS Vectors", vector_stack)).show();
ImagePlus imp3 = new ImagePlus("Velocities", velstack);
imp3.setOpenAsHyperStack(true);
imp3.setDimensions(2, 1, velframes / 2);
new CompositeImage(imp3, CompositeImage.COLOR).show();
}